CL65 FLT CREW HAD BEEN GIVEN A REROUTE. AFTER TKOF THE FLT CREW WERE NAVIGATING UTILIZING THE FMS; BUT WERE OFF COURSE. THE INTERMEDIATE FIXES FOR THE DEP TRANSITION HAD BEEN OMITTED.

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ON PUSHBACK WE WERE GIVEN A RE-RTE; THAT CHANGED THE TRANSITION OF THE ALAMO SIX DEP WE WERE USING TO THE LFK TRANSITION. ON TKOF I SELECTED THE NAV MODE AND THE FMS HAD SOMEHOW DELETED THE 2 MIDDLE FIXES (SEEDS; ELA). TAKING US DIRECT TO LFK IN PLACE OF THE CORRECT RADIALS. LEAVING SAT; WE WERE GIVEN A HDG TO INTERCEPT THE ALAMO SIX DEP AND THEN ON COURSE. WE PROCEEDED TO TURN TO THE HDG AND SELECTED THE NAV MODE. THE ACFT DECIDED TO TAKE US DIRECT LFK INSTEAD OF THE DEP ROUTING (SAT-SEEDS-ELA-LFK). AS WE WERE CLBING OUT WE WERE ASKED BY THE CTLR IF WE HAD BEEN CLRED TO ANYTHING OTHER THAN THE ALAMO SIX LFK TRANSITION; THAT WE WERE 3 MI OFF COURSE AND TO RESUME THE DEP. THE CTLR THEN POINTED OUT TFC; AND SHORTLY AFTER THAT SAID 'TFC ALERT; TURN R 120 DEGS OR 140 DEGS.' I IMMEDIATELY CLICKED OFF THE AUTOPLT; AND TURNED (WE DID NOT HAVE A TCAS TFC ALERT); WE WENT TO GREEN NEEDLES AND WENT BACK ON COURSE. THE CTR CTLR THEN INQUIRED AS TO WHAT OUR CLRNC WAS (WHICH HAD BEEN A RE-RTE AFTER PUSHBACK). WE THEN VERIFIED THE RTE WITH THE CTLR; THEN THE CTLR GAVE US FL290 AND A FREQ CHANGE. THE NEXT CTLR WENT ON TO VERIFY THE RTE AGAIN; THEN INQUIRED WHAT ALT WE WERE GIVEN. HE SEEMED TO NOT AGREE WITH OUR FL290 AND GAVE US FL390; WHICH WAS OUR FINAL ALT. UPON RECEIVING THE NEW RTE AND CLRNC (WHICH WE BOTH COPIED DOWN); I SHOULD HAVE VERIFIED THE ROUTING IN THE FMS. THE REASON THAT THIS WAS ACCIDENTALLY OVERLOOKED WAS THAT I WAS ON THE PHONE TO DISPATCH FINDING OUT OUR NEW MINIMUM FUEL NUMBER AND ENRTE FUEL BURN. NEXT TIME ON A RE-RTE I WILL VERIFY THE ROUTING IS IN THE FMS; LIKE I ALWAYS TO ANYTIME A RTE HAS BEEN PUT IN THE FMS.